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Identification of potential blood biomarkers for Parkinson’s disease by gene expression and DNA methylation data integration analysis
Changliang Wang; Liang Chen; Yang Yang; Menglei Zhang; Garry Wong
2019-02
Source PublicationCLINICAL EPIGENETICS
ISSN1868-7083
Volume11
AbstractBackground Blood-based gene expression or epigenetic biomarkers of Parkinson’s disease (PD) are highly desirable. However, accuracy and specificity need to be improved, and methods for the integration of gene expression with epigenetic data need to be developed in order to make this feasible. Methods Whole blood gene expression data and DNA methylation data were downloaded from Gene Expression Omnibus (GEO) database. A linear model was used to identify significantly differentially expressed genes (DEGs) and differentially methylated genes (DMGs) according to specific gene regions 5′—C—phosphate—G—3′ (CpGs) or all gene regions CpGs in PD. Gene set enrichment analysis was then applied to DEGs and DMGs. Subsequently, data integration analysis was performed to identify robust PD-associated blood biomarkers. Finally, the random forest algorithm and a leave-one-out cross validation method were performed to construct classifiers based on gene expression data integrated with methylation data. Results Eighty-five (85) significantly hypo-methylated and upregulated genes in PD patients compared to healthy controls were identified. The dominant hypo-methylated regions of these genes were significantly different. Some genes had a single dominant hypo-methylated region, while others had multiple dominant hypo-methylated regions. One gene expression classifier and two gene methylation classifiers based on all or dominant methylation-altered region CpGs were constructed. All have a good prediction power for PD. Conclusions Gene expression and methylation data integration analysis identified a blood-based 53-gene signature, which could be applied as a biomarker for PD.
KeywordParkinson's Disease Data Integration Dna Methylation Gene Expression
DOI10.1186/s13148-019-0621-5
Indexed BySCI
Language英语
WOS Research AreaOncology ; Genetics & Heredity
WOS SubjectOncology ; Genetics & Heredity
WOS IDWOS:000458409300002
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Cited Times [WOS]:3   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionFaculty of Health Sciences
AffiliationCancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R., Macau, China
First Author AffilicationFaculty of Health Sciences
Recommended Citation
GB/T 7714
Changliang Wang,Liang Chen,Yang Yang,et al. Identification of potential blood biomarkers for Parkinson’s disease by gene expression and DNA methylation data integration analysis[J]. CLINICAL EPIGENETICS,2019,11.
APA Changliang Wang,Liang Chen,Yang Yang,Menglei Zhang,&Garry Wong.(2019).Identification of potential blood biomarkers for Parkinson’s disease by gene expression and DNA methylation data integration analysis.CLINICAL EPIGENETICS,11.
MLA Changliang Wang,et al."Identification of potential blood biomarkers for Parkinson’s disease by gene expression and DNA methylation data integration analysis".CLINICAL EPIGENETICS 11(2019).
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